TB Profiler
This tool processes raw sequence data to infer strain type and identify known drug resistance markers.
A stand alone version of this tool is now available and can now be run on linux or mac. Installation instructions can be found on GitHub and on the bioconda page.



This tool is for Research Use Only. Data and information provided through use of this tool are not intended for medical purpose or objective and should not be used for clinical diagnosis, patient management, or human clinical trials.
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Single nucleotide polymorphisms (SNPs) in coding regions are annotated using the reference amino acid, codon number and alternative amino acid (e.g. Ser315Thr in katG). SNPs in non-coding regions (i.e. RNA genes and intergenic regions) are annotated using the reference nucleotide, gene coordinate and alternative nucleotide (e.g. A1401G in rrs or C-37A in eis promoter). Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG).
Name: 5dd3ba9ec9fd2
Sample: 5dd3ba9ec9fd2

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Summary
ID: 5dd3ba9ec9fd2
Date: Tue Nov 19 09:54:18 2019
Strain: lineage4.6.2.2
Drug-resistance: Sensitive

Drug1ResistanceSupporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2FamilyMain SpoligotypeRDS
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.6Euro-AmericanT;LAMNone
lineage4.6.2Euro-AmericanT;LAMRD726
lineage4.6.2.2Euro-American (Cameroon)LAM10-CAMRD726

Mutations in candidate genes:
GeneChromosome PositionMutationEstimated fraction
gyrA7362p.Glu21Gln1.000
gyrA7585p.Ser95Thr1.000
gyrA9304p.Gly668Asp1.000
rpsL781395c.-165T>C1.000
rrs1472172r.327t>c0.183
rrs1472181r.336g>a0.168
rrs1472214r.369c>g0.228
rrs1472235r.390g>c0.198
rrs1472240r.395g>c0.190
rrs1472242r.397c>t0.186
rrs1472251r.406g>a0.148
rrs1472253r.408g>t0.152
rrs1472259r.414c>a0.154
rrs1472266r.421c>a0.144
rrs1472338r.493a>c0.204
rrs1472344r.499c>t0.224
rrs1472349r.504a>t0.240
rrs1472374r.529t>a0.228
rrs1472379r.534t>g0.231
rrs1472382r.537g>t0.237
rrs1472391r.546c>t0.224
rrs1472598r.753a>t0.186
rrs1472616r.771g>a0.248
rrs1472734r.889c>t0.202
rrs1472741r.896g>a0.189
rrs1472742r.897c>t0.212
rrs1472781r.936c>t0.216
rrs1472793r.948a>t0.216
rrs1472803r.958t>a0.200
rrs1472812r.967a>c0.197
rrs1472887r.1042g>c0.236
rrs1473038r.1193a>c0.252
rrs1473044r.1199c>g0.241
rrs1473173r.1328c>t0.185
rrs1473177r.1332g>a0.238
rrs1473202r.1357c>t0.250
rrl1474199r.542g>a0.170
rrl1474201r.544t>c0.170
rrl1474202r.545t>a0.170
rrl1474218r.561t>a0.224
rrl1474228r.571t>c0.190
rrl1474235r.578g>c0.174
rrl1474249r.592g>t0.168
rrl1474252r.595t>a0.162
rrl1474264r.607t>g0.160
rrl1474265r.608g>a0.160
rrl1475526r.1869c>t0.174
rrl1475538r.1881t>c0.135
rrl1475539r.1882a>t0.141
rrl1475540r.1883c>t0.141
rrl1475545r.1888t>g0.137
rrl1475571r.1914a>t0.168
rrl1475707r.2050t>c0.148
rrl1475713r.2056c>g0.150
rrl1475716r.2059a>t0.144
rrl1475803r.2146t>c0.224
rrl1475804r.2147g>c0.224
rrl1475816r.2159c>g0.248
rrl1475817r.2160a>g0.250
rrl1476252r.2595t>g0.140
rrl1476260r.2603a>g0.137
rrl1476266r.2609g>a0.140
rrl1476336r.2679c>g0.214
rrl1476356r.2699c>g0.208
rrl1476357r.2700t>a0.222
rrl1476358r.2701t>c0.176
rrl1476382r.2725a>g0.195
rrl1476384r.2727g>t0.204
rrl1476404r.2747g>a0.209
rrl1476408r.2751g>a0.261
rrl1476442r.2785t>a0.210
rrl1476443r.2786g>t0.225
rrl1476455r.2798c>a0.191
rrl1476456r.2799a>t0.189
rrl1476466r.2809c>t0.214
rrl1476470r.2813c>t0.222
rrl1476474r.2817c>t0.184
rrl1476481r.2824t>c0.188
tlyA1917972c.33A>G1.000
thyX3067474p.Pro158Ala1.000
alr3841662c.-242A>G0.217
alr3841663c.-243G>A0.214
embC4242643c.2781C>T1.000
embB4246584p.Arg24Pro0.600
ethA4326739c.735G>C1.000
ethR4328004c.456G>A1.000

Analysis pipeline specifications

TBProfiler Version: 2.1.1

AnalysisProgram
Mappingbwa
Variant CallingBCFtools


Log

Drug Details
The estimated accuracy of drug resistance predictions is:

Drug1Sensitivity (%)Specificity (%)
Isoniazid 92.8 (89.9-95.7)100 (100-100)
Rifampicin 96.2 (93.9-98.5)98.1 (96.8-99.4)
Ethambutal 88.7 (83.6-93.8)81.7 (77.6-85.8)
Pyrazinamide70.9 (62.4-79.4)93.9 (90.6-97.2)
Streptomycin87.1 (82.7-91.5)89.7 (86.0-93.4)
Ethionamide 73.6 (66.7-80.5)93.3 (89.6-97.0)
Moxifloxacin60.0 (29.6-90.4)68.7 (52.6-84.8)
Ofloxacin 85.5 (79.1-91.9)94.9 (91.8-98.0)
Amikacin 82.9 (74.4-91.4)98.3 (96.0-100)
Capreomycin 60.7 (50.6-70.8)90.7 (87.2-94.2)
Kanamycin 87.3 (81.3-93.3)93.4 (89.9-96.9)
Para-aminosalisylic acidNot determinedNot determined
Linezolid Not determinedNot determined
Clofazimine Not determinedNot determined
Bedaquiline Not determinedNot determined
Multi drug resistance91.2 (87.8-94.6)98.4 (97.2-99.6)
Extremely drug resistance75.9 (64.5-87.3)98.4 (97.3-99.5)

Lineages
Lineage2LocationStrainRD type
lineage1Indo-OceanicEAIRD239
lineage1.1Indo-OceanicEAI3;EAI4;EAI5;EAI6RD239
lineage1.1.1Indo-OceanicEAI4;EAI5RD239
lineage1.1.1.1Indo-OceanicEAI4;ZERORD239
lineage1.1.2Indo-OceanicEAI3;EAI5RD239
lineage1.1.3Indo-OceanicEAI6RD239
lineage1.2Indo-OceanicEAI1;EAI2RD239
lineage1.2.1Indo-OceanicEAI2RD239
lineage1.2.2Indo-OceanicEAI1RD239
lineage2East-AsianBeijingRD105
lineage2.1East-Asian (non-Beijing)NoneNone
lineage2.2East-Asian (Beijing)Beijing-RD207RD105;RD207
lineage2.2.2East-Asian (Beijing)Beijing-RD105/RD207RD105;RD207
lineage2.2.1East-Asian (Beijing)Beijing-RD181RD105;RD207;RD181
lineage2.2.1.2East-Asian (Beijing)Beijing-RD142RD105;RD207;RD181;RD142
lineage2.2.1.1East-Asian (Beijing)Beijing-RD150RD105;RD207;RD181;RD150
lineage3East-African-IndianCASRD750
lineage3.1East-African-IndianNon-CAS1-DelhiRD750
lineage3.1.1East-African-IndianCAS1-KiliRD750
lineage3.1.2East-African-IndianCAS;CAS2RD750
lineage3.1.2.1East-African-IndianCAS2RD750
lineage3.1.2.2East-African-IndianCASRD750
lineage4Euro-AmericanLAM;T;S;X;HNone
lineage4.1Euro-AmericanT;X;HNone
lineage4.1.2Euro-American (X-type)T;HNone
lineage4.1.2.1Euro-American (X-type)T1;H1RD182
lineage4.1.1Euro-American (X-type)X1;X2;X3None
lineage4.1.1.2Euro-American (X-type)X1None
lineage4.1.1.1Euro-American (X-type)X2RD183
lineage4.1.1.3Euro-American (Haarlem)X1;X3RD193
lineage4.2Euro-AmericanH;T;LAMNone
lineage4.2.2Euro-American (Ural)T;LAM7-TURNone
lineage4.2.2.1Euro-AmericanLAM7-TURNone
lineage4.2.1Euro-American (TUR)H3;H4None
lineage4.3Euro-American (LAM)mainly-LAMNone
lineage4.3.1Euro-American (LAM)LAM9None
lineage4.3.3Euro-American (LAM)LAM;TRD115
lineage4.3.4Euro-American (LAM)LAMRD174
lineage4.3.4.1Euro-American (LAM)LAM1;LAM2RD174
lineage4.3.4.2Euro-American (LAM)LAM1;LAM4;LAM11RD174
lineage4.3.4.2.1Euro-American (LAM)LAM11RD174
lineage4.3.2Euro-American (LAM)LAM3None
lineage4.3.2.1Euro-American (LAM)LAM3RD761
lineage4.4Euro-AmericanS;TNone
lineage4.4.2Euro-AmericanT1;T2None
lineage4.4.1Euro-American (S-type)S;TNone
lineage4.4.1.2Euro-AmericanT1None
lineage4.4.1.1Euro-AmericanS;OrphansNone
lineage4.5Euro-AmericanH;TRD122
lineage4.6Euro-AmericanT;LAMNone
lineage4.6.1Euro-American (Uganda)T2RD724
lineage4.6.1.1Euro-American T2-UgandaRD724
lineage4.6.1.2Euro-AmericanT2RD724
lineage4.6.2Euro-AmericanT;LAMRD726
lineage4.6.2.1Euro-AmericanT3RD726
lineage4.6.2.2Euro-American (Cameroon)LAM10-CAMRD726
lineage4.7Euro-American (mainly T)T1;T5None
lineage4.8Euro-American (mainly T)T1;T2;T3;T5RD219
lineage4.9Euro-American (H37Rv-like)T1None
lineage5West-Africa 1AFRI_2;AFRI_3RD711
lineage6West-Africa 2AFRI_1RD702
lineage7Lineage 7NoneNone
lineageBOVM. bovisBOV_1;BOV_2None

Citations
1. Coll F, et al. Rapid determination of anti-tuberculosis drug resistance from whole genome sequences. Genome Medicine (in press)
2. Coll F, et al. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains. Nature Communications 2014.

Disclaimer
This tool is for Research Use Only and is offered free for use. The London School of Hygiene and Tropical Medicine shall have no liability for any loss or damages of any kind, however sustained relating to the use of this tool.
© 2019 London School of Hygiene and Tropical Medicine;